Protein Molecular Weight Calculator

Frequently Asked Questions

How is protein molecular weight calculated from sequence?

Each amino acid residue has a known average mass in Daltons. The protein MW equals the sum of all residue masses plus 18.015 Da for the terminal water molecule (H at the N-terminus and OH at the C-terminus).

What is the difference between average and monoisotopic mass?

Average mass uses the natural isotopic abundance of each element and is used for most lab work such as gel estimation and protein purification. Monoisotopic mass uses only the lightest isotope of each element and is used in mass spectrometry for high-resolution identification.

How accurate is this estimate compared to the actual protein?

The sequence-based calculation gives the unmodified mass. Post-translational modifications (glycosylation, phosphorylation, disulfide bonds) and signal peptide cleavage will change the actual mass. Signal peptides add mass in silico but are removed in vivo.

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Estimates for informational purposes only.

Important Disclaimer: Estimates for informational purposes only.

This calculator provides estimates for informational purposes only. Results are based on assumptions and may not reflect actual outcomes. Consult qualified professionals in relevant fields before making important decisions based on these results.

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How This Calculator Works

This calculator estimates the molecular weight of a protein from its primary sequence using average isotopic masses for each of the 20 standard amino acid residues. A residue mass is the mass of the amino acid after losing one water molecule during peptide bond formation. The calculator sums those residue masses and adds back 18.015 Da for the single water molecule at the free N-terminus and C-terminus of the intact polypeptide.

Paste or type your sequence using standard IUPAC single-letter codes. Whitespace and line breaks are stripped automatically. The sequence must contain only the 20 canonical amino acids (A C D E F G H I K L M N P Q R S T V W Y).

Average vs Monoisotopic Mass

There are two conventions for reporting amino acid masses. Average masses use the natural isotopic abundances of each element - for example, carbon is about 98.9% carbon-12 and 1.1% carbon-13, so average carbon has a mass of 12.011 Da rather than exactly 12. These are the values used here and they match the mass reading you get from most protein gel bands calibrated with standard ladders.

Monoisotopic masses count only the lightest isotope of every element (carbon-12, hydrogen-1, nitrogen-14, oxygen-16, sulfur-32). They are used in mass spectrometry where the instrument resolves individual isotope peaks. For proteins larger than about 2,000 Da, the isotope envelope becomes broad and the monoisotopic peak is no longer the tallest, so average masses are more practical for routine MW estimation.

Common Mistakes

Using three-letter codes (Met, Ala...) instead of single-letter codes - the calculator expects single-letter only.

Including non-standard residues such as selenocysteine (U), pyrrolysine (O), or ambiguity codes (B, Z, X) - remove or substitute these before calculating.

Forgetting that the calculated MW is for the unmodified, unfolded chain. Post-translational modifications (glycosylation, phosphorylation, disulfide bonds) change the actual mass.

Confusing Da and kDa - a 50,000 Da protein is 50 kDa, which is a common reference size on gel ladders.

Tips & FAQ

What if my protein has disulfide bonds? Each disulfide bond removes 2.016 Da (two hydrogens). Subtract 2.016 Da per bond from the result.

How accurate is this estimate? Within 0.01% of the true average molecular weight for an unmodified protein. The main source of error in practice is an incorrect or incomplete sequence.

Can I calculate the MW of a fragment? Yes - paste only the residues in that fragment. The formula applies to any peptide regardless of length.

Why does MW matter in the lab? It determines the expected position on an SDS-PAGE gel, the retention time in size-exclusion chromatography, and the stoichiometry for protein-ligand binding assays.

Protein Molecular Weight Calculator

Frequently Asked Questions

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